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Rosetta 3 - General

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Normal topic I'm a total beginner to Rosetta 3.2 and there are no tutorials for me to follow. Can someone help.? =)
by monos_morpheus » Wed, 2011-02-02 08:11 		12
 11,493 by monos_morpheus
Mon, 2014-04-21 06:47
Normal topic I've got two doubts
by jrcf » Sun, 2016-01-10 07:45 		1
 2,076 by smlewis
Sun, 2016-01-10 10:02
Normal topic Icouldnot find DDMI protocol for design protein
by ladimafakher » Mon, 2018-02-12 09:22 		1
 1,786 by rmoretti
Mon, 2018-02-12 09:39
Normal topic idealization error
by albumns » Mon, 2011-02-07 01:28 		1
 2,220 by smlewis
Mon, 2014-04-21 06:47
Normal topic Identical decoys
by aroop » Tue, 2012-09-25 12:50 		4
 4,820 by smlewis
Mon, 2014-04-21 06:47
Normal topic ignore loops on threading
by fred » Tue, 2014-11-11 11:33 		5
 5,430 by rmoretti
Tue, 2014-11-18 10:01
Normal topic Illegal attempt to score with non-identical atom set between pose and etable
by ng98 » Fri, 2024-06-07 03:22 		1
 127 by rmoretti
Tue, 2024-06-11 02:45
Normal topic incomparable ddG values
by ela » Fri, 2018-08-31 02:53 		0
 1,282 by ela
Fri, 2018-08-31 02:53
Normal topic Inconsistent scoring by "aa_composition" term
by chenna » Thu, 2022-02-24 03:00 		1
 961 by vmulligan
Thu, 2022-03-03 18:48
Normal topic industrial example of ROSETTA modeled protein
by banshee » Sat, 2016-04-23 23:40 		5
 5,405 by banshee
Tue, 2016-04-26 00:47
Normal topic Ineffective Constraints
by Sandy » Tue, 2017-09-05 19:36 		2
 2,451 by CameronJA
Wed, 2022-01-19 20:50
Normal topic Information about “membrane_highres_Menv_smooth.wts”
by Groros » Sun, 2011-10-02 03:59 		3
 3,970 by smlewis
Mon, 2014-04-21 06:47
Normal topic input secondary structure prediction to AbinitioRelax
by biofisikx » Mon, 2010-08-09 12:36 		2
 2,735 by biofisikx
Mon, 2014-04-21 06:47
Normal topic input_score_filter not taken by program cluster ?
by Anonymous » Mon, 2012-06-11 09:14 		9
 9,435 by attesor
Fri, 2014-10-31 04:49
Normal topic Installing on windows using MinGW
by abdullah_ahmed » Wed, 2010-09-15 08:45 		1
 2,058 by smlewis
Mon, 2014-04-21 06:47
Normal topic Installing rosetta 3.0
by dalemu » Thu, 2009-09-24 13:28 		1
 2,912 by smlewis
Mon, 2014-04-21 06:47
Normal topic Installing Rosetta Abinitio make_fragments.pl
by ctaylor » Thu, 2009-09-17 09:20 		2
 3,532 by ctaylor
Mon, 2014-04-21 06:47
Normal topic Intel Compiler and OS X Intel
by bene » Tue, 2009-10-20 10:20 		1
 2,622 by smlewis
Mon, 2014-04-21 06:47
Normal topic Intel MPI: early exit due to job process stopped.
by jackzzs » Mon, 2023-05-15 02:57 		0
 1,402 by jackzzs
Mon, 2023-05-15 03:17
Normal topic Interface energy vs binding energy
by Apiwat » Wed, 2014-02-05 00:47 		2
 6,433 by Apiwat
Sat, 2014-02-08 01:41
Normal topic Interface rmsd calculation Irms
by mahajanr » Wed, 2010-07-07 18:24 		5
 8,062 by mahajanr
Mon, 2014-04-21 06:47
Normal topic Interface scores comparison
by NingNing » Tue, 2022-08-09 17:36 		0
 546 by NingNing
Tue, 2022-08-09 17:36
Normal topic InterfaceAnalyzer atom subset
by Parker.deWaal » Sun, 2016-03-13 13:41 		2
 2,914 by rmoretti
Mon, 2016-03-14 07:58
Normal topic InterfaceAnalyzer packstat score = 0.000
by vmc99 » Fri, 2018-11-16 11:30 		11
 8,998 by SenyorDrew
Wed, 2019-06-12 14:10
Normal topic InterfaceAnalyzer total score = 0.000
by vmc99 » Wed, 2019-06-12 14:06 		3
 3,386 by jadolfbr
Wed, 2019-06-12 20:17
Normal topic Intermediate file insertion
by exchhattu » Wed, 2009-09-02 18:44 		2
 2,827 by exchhattu
Mon, 2014-04-21 06:47
Normal topic Internal error while running AbinitioRelax
by Subhrodeep Saha » Sun, 2021-06-13 03:44 		1
 1,369 by rmoretti
Wed, 2021-06-23 02:17
Normal topic Interpreting decoy ensemble
by lah435 » Wed, 2015-06-10 10:25 		1
 2,067 by rmoretti
Fri, 2015-07-03 13:51
Normal topic interpreting score values in silent output file after running abinitiorelax
by burkheadlab » Wed, 2011-03-09 15:42 		3
 3,665 by smlewis
Mon, 2014-04-21 06:47
Normal topic intrensic disrodered proteins
by ac.research » Thu, 2019-04-04 07:20 		1
 1,637 by vmulligan
Mon, 2019-04-08 14:49
Normal topic Introduction or tutorial about RosettaMatch
by kwak » Thu, 2010-10-21 06:37 		4
 6,580 by kwak
Mon, 2014-04-21 06:47
Normal topic Is cis-Glycine okay?
by matteoferla » Tue, 2019-11-19 07:26 		5
 3,887 by matteoferla
Wed, 2019-11-20 02:32
Normal topic Is CST_Design required for enzdes protocol?
by dasdevashishdas » Mon, 2018-09-03 00:51 		2
 2,450 by dasdevashishdas
Thu, 2018-09-27 03:35
Normal topic Is it better to have smaller nstruct but many runs?
by Loki01 » Mon, 2018-11-19 11:50 		3
 2,703 by smlewis
Mon, 2018-11-19 13:20
Normal topic Is it CS-HM Rosetta restraint derivation i.e cm_scripts in Rosetta 3.3 bundles?
by nh_prt » Tue, 2013-03-26 12:22 		3
 3,710 by smlewis
Mon, 2014-04-21 06:47
Normal topic Is it impossible to use the ddg_monomer function on a non-monomeric structure?
by Wexter300 » Sat, 2024-05-25 14:16 		1
 111 by rmoretti
Thu, 2024-06-20 13:24
Normal topic is it possbile to cluster pdb files?
by albumns » Wed, 2010-10-06 02:38 		3
 5,453 by smlewis
Mon, 2014-04-21 06:47
Normal topic is it possible to ab initio only a part of a protein?
by albumns » Sun, 2011-02-13 08:10 		6
 5,159 by albumns
Mon, 2014-04-21 06:47
Normal topic Is it possible to do Abinitio folding from a linear structure.?
by monos_morpheus » Sat, 2011-04-16 09:13 		11
 9,864 by monos_morpheus
Mon, 2014-04-21 06:47
Hot topic Is it possible to do alanine scanning in Rosetta 3.2.1.?
by monos_morpheus » Tue, 2011-04-12 02:36 		21
 22,633 by smlewis
Mon, 2014-04-21 06:47
Normal topic is it possible to generate models without hydrogen?
by albumns » Fri, 2012-03-02 12:24 		9
 8,552 by albumns
Mon, 2014-04-21 06:47
Normal topic Is it possible to use two broker files
by kalabharath » Wed, 2011-06-08 01:01 		1
 2,495 by smlewis
Mon, 2014-04-21 06:47
Normal topic Is the Fold&Dock protocol availabe in Rosetta3.1
by justin » Mon, 2011-01-17 02:41 		2
 2,606 by smlewis
Mon, 2014-04-21 06:47
Normal topic Is the packer aware of non canonical amino acids?
by krdav » Tue, 2016-08-16 08:16 		7
 6,758 by krdav
Wed, 2016-08-17 12:57
Normal topic is the RosettaNMR protocol available in Rosetta 3.x?
by murgantia » Wed, 2011-01-26 00:39 		1
 2,258 by smlewis
Mon, 2014-04-21 06:47
Normal topic is there a preferred way to enforce an hydrogen bond ?
by logandonaldson » Wed, 2013-03-20 13:14 		2
 2,924 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Is there a way to calculate chi1 and chi1+chi differences between two structures?
by sn » Thu, 2017-04-20 21:46 		1
 2,185 by rmoretti
Fri, 2017-04-21 07:52
Normal topic Is there any significant improvement of model generation in rosetta3.4 comparing to rosetta3.3?
by jiongzhang » Fri, 2012-04-20 13:35 		2
 3,006 by rmoretti
Mon, 2014-04-21 06:47
Normal topic IS there any source code about protein structure prediction with only sequences information?
by ylwang » Mon, 2019-07-08 02:36 		1
 1,650 by rmoretti
Mon, 2019-07-08 08:05
Normal topic Is there other online server for generate fragment?
by ylwang » Wed, 2020-04-01 01:39 		1
 1,520 by rmoretti
Wed, 2020-04-01 10:10
Normal topic Issue with Loop Analyzer Mover ouput
by abhi_pe_acharya » Mon, 2018-04-30 09:55 		2
 2,157 by abhi_pe_acharya
Mon, 2018-04-30 22:54
Normal topic Issues running the Matcher in 3.4 and 3.5
by Jhreed » Tue, 2015-05-26 11:38 		1
 2,219 by rmoretti
Wed, 2015-06-17 12:43
Normal topic Issues with angle Constraints during Docking
by LeonhardJS » Thu, 2021-01-28 04:40 		2
 1,847 by LeonhardJS
Fri, 2021-01-29 01:12
Normal topic Issues with residues and structure changing with FlexPepDock; is this normal?
by rnelson » Tue, 2017-08-08 10:06 		1
 1,883 by Ora Schueler-Furman
Sun, 2017-08-20 00:54
Normal topic Issues with rosetta numbering and keeping ligand when relaxing molecule.
by Wexter300 » Sun, 2024-04-28 14:37 		5
 540 by rmoretti
Thu, 2024-06-20 13:28
Normal topic Iterative local rebuilding vs automated structure refinement
by ahmadkhalifa » Fri, 2018-09-14 07:44 		4
 3,732 by rmoretti
Wed, 2018-11-21 14:11
Normal topic I_sc
by Soler » Sat, 2022-02-12 00:16 		1
 1,176 by rmoretti
Fri, 2022-02-18 11:14
Normal topic jd2 time out error
by ytao » Mon, 2013-03-04 20:47 		2
 2,827 by ytao
Mon, 2014-04-21 06:47
Normal topic JD3 FastRelax over MPI - crashes on relax completion/before writing output
by aduffy33 » Tue, 2024-03-12 12:51 		0
 253 by aduffy33
Tue, 2024-03-12 12:52
Normal topic JD3 w/ Silent file output crashing - Option filename not found
by aduffy33 » Mon, 2023-10-30 13:40 		2
 546 by aduffy33
Mon, 2023-10-30 15:35
Normal topic Job Distribution Error
by ac.research » Mon, 2020-02-10 08:22 		2
 2,150 by ac.research
Fri, 2020-02-14 23:33
Normal topic Jump::random_trans strange behavior
by SergeyP » Tue, 2015-11-03 07:56 		2
 2,740 by SergeyP
Sat, 2015-12-19 05:20
Normal topic keep ATP in the kinase-peptide structure while docking
by ziqi1234 » Fri, 2017-11-10 04:04 		0
 1,178 by ziqi1234
Fri, 2017-11-10 04:04
Normal topic keep crystal structure hydrogens
by gw » Wed, 2011-07-20 03:54 		2
 3,373 by gw
Mon, 2014-04-21 06:47
Normal topic kinematic loop modeling/sequence design keeps crashing with segmentation fault
by banshee » Thu, 2013-03-28 09:52 		8
 8,597 by smlewis
Mon, 2014-04-21 06:47
Normal topic Knowledge check on steric effects
by pachecoj » Thu, 2014-10-16 09:13 		1
 2,463 by rmoretti
Thu, 2014-10-16 10:33
Normal topic known disulfides in Remodel sequence
by matteoferla » Mon, 2018-09-10 06:43 		1
 1,904 by matteoferla
Thu, 2018-09-13 06:21
Normal topic latest version of rosetta--unable to build models
by pramod » Mon, 2014-11-03 11:40 		10
 11,249 by jadolfbr
Wed, 2014-11-26 11:40
Normal topic lDDT: local Distance Difference Test implemented?
by ipetrik_ambry » Wed, 2017-12-06 13:11 		0
 1,386 by ipetrik_ambry
Wed, 2017-12-06 13:11
Normal topic LHOC script problem in Rosetta Antibody
by ziheng@mit.edu » Thu, 2019-04-25 14:19 		3
 2,484 by Brian Wiley
Sat, 2023-02-04 23:26
Normal topic Library of unnatural amino acid parameters
by saxen » Mon, 2017-04-17 11:08 		1
 3,898 by smlewis
Tue, 2017-04-18 08:33
Normal topic Ligand being read as part of protein structure
by MarkusAurelius » Thu, 2021-04-01 11:00 		2
 1,815 by MarkusAurelius
Fri, 2021-04-02 11:44
Normal topic Ligand conformations file in docking
by rosa » Fri, 2013-07-12 09:21 		4
 5,544 by rosa
Mon, 2014-04-21 06:48
Normal topic ligand dock residue selection
by Silice » Wed, 2009-08-12 08:57 		2
 3,005 by frichter
Mon, 2014-04-21 06:47
Normal topic ligand docking
by hong wei » Thu, 2021-11-18 05:01 		2
 1,432 by hong wei
Thu, 2021-11-25 02:46
Normal topic ligand docking error
by YuFei » Wed, 2020-04-22 17:27 		0
 1,008 by YuFei
Wed, 2020-04-22 17:27
Hot topic Ligand Docking Positive Control: wt ligand
by Basantab » Thu, 2011-10-27 13:36 		16
 14,594 by Basantab
Mon, 2014-04-21 06:47
Normal topic Ligand Docking with Orphan GPCR
by marsaa » Thu, 2016-10-13 07:45 		1
 2,461 by rmoretti
Fri, 2016-10-14 16:43
Normal topic ligand docking with rosetta_scripts.linuxgccrelease
by xpzhang » Thu, 2015-02-26 10:57 		3
 4,376 by rmoretti
Mon, 2015-03-30 16:58
Normal topic Ligand docking: how to generate the crystal_complex.pdb with hydrogens added
by nhinguyen26 » Wed, 2020-06-17 15:03 		1
 1,471 by matteoferla
Sat, 2020-06-20 03:56
Normal topic ligand flexibility
by dave » Thu, 2015-02-12 08:48 		1
 2,287 by rmoretti
Wed, 2015-02-18 09:17
Normal topic Ligand question - aromatic bonds not being enforced?
by Rick_Baker » Wed, 2019-09-11 09:08 		1
 1,598 by Rick_Baker
Wed, 2019-09-11 15:35
Normal topic Linker problems when building mini
by assaff » Mon, 2009-10-12 01:07 		6
 5,842 by smlewis
Mon, 2014-04-21 06:47
Normal topic local refinement
by mahajanr » Mon, 2010-07-19 15:04 		1
 2,274 by smlewis
Mon, 2014-04-21 06:47
Normal topic location of define_interface.py
by rohi » Mon, 2020-10-26 19:42 		3
 2,137 by rmoretti
Tue, 2023-05-09 15:32
Normal topic log files
by shadrinams » Fri, 2018-01-26 07:29 		7
 7,220 by shadrinams
Mon, 2018-02-12 11:47
Normal topic Looking for a pdb....
by MarkW » Mon, 2014-10-13 15:45 		8
 8,555 by rmoretti
Mon, 2014-11-03 16:30
Normal topic Looking for collaboration.
by ac.research » Mon, 2017-03-06 04:54 		1
 1,943 by rmoretti
Mon, 2017-03-06 08:37
Normal topic loop design
by varma » Sun, 2012-11-04 21:25 		2
 4,138 by varma
Mon, 2014-04-21 06:47
Normal topic Loop extensions at the end of chains
by japgar » Mon, 2010-07-26 12:35 		4
 4,361 by japgar
Mon, 2014-04-21 06:47
Normal topic loop file
by banshee » Tue, 2013-06-04 13:26 		2
 2,879 by banshee
Mon, 2014-04-21 06:48
Normal topic Loop Insertion/Extension using rosetta suite
by bharat_46010 » Mon, 2011-02-28 04:45 		1
 2,180 by smlewis
Mon, 2014-04-21 06:47
Hot topic loop model error
by albumns » Sun, 2011-04-03 00:26 		21
 20,891 by rmoretti
Fri, 2015-12-18 14:26
Normal topic Loop modeling
by Robertofg » Tue, 2022-11-22 00:34 		0
 657 by Robertofg
Tue, 2022-11-22 00:34
Normal topic loop modeling
by bharat_46010 » Thu, 2015-08-06 01:34 		1
 2,073 by rmoretti
Thu, 2015-08-06 09:28
Normal topic loop modeling
by MRH » Thu, 2013-08-22 23:19 		3
 4,382 by MRH
Mon, 2014-04-21 06:48
Normal topic loop modeling
by isengupta13 » Wed, 2011-06-01 15:00 		3
 4,042 by smlewis
Mon, 2014-04-21 06:47
Normal topic Loop Modeling
by ctaylor » Fri, 2009-12-18 11:42 		3
 3,609 by ctaylor
Mon, 2014-04-21 06:47
Normal topic Loop Modeling Deletes Residues
by Julix » Wed, 2012-09-05 10:14 		7
 7,075 by smlewis
Mon, 2014-04-21 06:47
Normal topic Loop modeling FLAGS
by jklett » Fri, 2009-12-04 02:45 		3
 3,729 by jklett
Mon, 2014-04-21 06:47